+Open data
-Basic information
Entry | Database: PDB / ID: 6rwa | ||||||
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Title | Cryo-EM structure of Photorhabdus luminescens TcdA4 | ||||||
Components | TcdA4 | ||||||
Keywords | TOXIN / membrane permeation / translocation / complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Photorhabdus luminescens (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Roderer, D. / Leidreiter, F. / Gatsogiannis, C. / Meusch, D. / Benz, R. / Raunser, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Adv / Year: 2019 Title: Common architecture of Tc toxins from human and insect pathogenic bacteria. Authors: F Leidreiter / D Roderer / D Meusch / C Gatsogiannis / R Benz / S Raunser / Abstract: Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution ...Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution structures of TcAs from different bacteria suggest a considerable difference in their architecture and possibly in their mechanism of action. Here, we present high-resolution structures of five TcAs from insect and human pathogens, which show a similar overall composition and domain organization. Essential structural features, including a trefoil protein knot, are present in all TcAs, suggesting a common mechanism of action. All TcAs form functional pores and can be combined with TcB-TcC subunits from other species to form active chimeric holotoxins. We identified a conserved ionic pair that stabilizes the shell, likely operating as a strong latch that only springs open after destabilization of other regions. Our results provide new insights into the architecture and mechanism of the Tc toxin family. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6rwa.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6rwa.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 6rwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rwa_validation.pdf.gz | 840.6 KB | Display | wwPDB validaton report |
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Full document | 6rwa_full_validation.pdf.gz | 941.7 KB | Display | |
Data in XML | 6rwa_validation.xml.gz | 277.9 KB | Display | |
Data in CIF | 6rwa_validation.cif.gz | 425.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/6rwa ftp://data.pdbj.org/pub/pdb/validation_reports/rw/6rwa | HTTPS FTP |
-Related structure data
Related structure data | 10036MC 6rw6C 6rw8C 6rw9C 6rwbC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 270695.250 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdA4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GF92 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: P. luminescens TcdA4 pentamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 1.4 MDa / Experimental value: NO |
Source (natural) | Organism: Photorhabdus luminescens (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 1 sec. / Electron dose: 30.7 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | |||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | |||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35857 / Symmetry type: POINT | |||||||||||||||
Atomic model building | PDB-ID: 1VW1 1vw1 Accession code: 1VW1 / Source name: PDB / Type: experimental model |